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rs1558902

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001080432.3(FTO):c.46-40478T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 151,962 control chromosomes in the GnomAD database, including 8,797 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.31 ( 8797 hom., cov: 31)

Consequence

FTO
NM_001080432.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.355
Variant links:
Genes affected
FTO (HGNC:24678): (FTO alpha-ketoglutarate dependent dioxygenase) This gene is a nuclear protein of the AlkB related non-haem iron and 2-oxoglutarate-dependent oxygenase superfamily but the exact physiological function of this gene is not known. Other non-heme iron enzymes function to reverse alkylated DNA and RNA damage by oxidative demethylation. Studies in mice and humans indicate a role in nervous and cardiovascular systems and a strong association with body mass index, obesity risk, and type 2 diabetes. [provided by RefSeq, Jul 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FTONM_001080432.3 linkuse as main transcriptc.46-40478T>A intron_variant ENST00000471389.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FTOENST00000471389.6 linkuse as main transcriptc.46-40478T>A intron_variant 1 NM_001080432.3 P1Q9C0B1-1

Frequencies

GnomAD3 genomes
AF:
0.309
AC:
46860
AN:
151844
Hom.:
8801
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.102
Gnomad AMI
AF:
0.489
Gnomad AMR
AF:
0.289
Gnomad ASJ
AF:
0.511
Gnomad EAS
AF:
0.154
Gnomad SAS
AF:
0.332
Gnomad FIN
AF:
0.424
Gnomad MID
AF:
0.389
Gnomad NFE
AF:
0.417
Gnomad OTH
AF:
0.337
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.308
AC:
46845
AN:
151962
Hom.:
8797
Cov.:
31
AF XY:
0.309
AC XY:
22974
AN XY:
74258
show subpopulations
Gnomad4 AFR
AF:
0.102
Gnomad4 AMR
AF:
0.289
Gnomad4 ASJ
AF:
0.511
Gnomad4 EAS
AF:
0.154
Gnomad4 SAS
AF:
0.331
Gnomad4 FIN
AF:
0.424
Gnomad4 NFE
AF:
0.417
Gnomad4 OTH
AF:
0.338
Alfa
AF:
0.390
Hom.:
6856
Bravo
AF:
0.285
Asia WGS
AF:
0.270
AC:
941
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
1.4
Dann
Benign
0.65

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1558902; hg19: chr16-53803574; API